Cysteine proteases represent an enzymatic class of proteins that catalyze the hydrolysis of peptide bonds by a nucleophilic sulfhydryl group of a cysteine residue in the active site of the enzyme. Several normal and disease processes in mammals have been associated with cysteine protease activity and include, but are not limited to: osteoporosis, osteoarthritis (Inui, T., O. Ishibashi, J Biol Chem 1997, 272(13), 8109–12; Saftig, P., E. Hunziker, et al., Adv Exp Med Biol 2000+ADs 2000, 477, 293–303; Saftig, P., E. Hunziker, et al., Proc Natl Acad Sci USA 1998, 95(23), 13453–8), periodontal diseases, Paget's disease, atherosclerosis (Jormsjo, S., D. M. Wuttge, et al., Am J Pathol 2002 161(3), 939–45), multiple sclerosis (Beck, H., G. Schwarz, et al., Eur J Immunol 2001, 31(12), 3726–36), rheumatoid arthritis (Nakagawa, T. Y., W. H. Brissette, et al., Immunity 1999, 10(2), 207–17; Hou, W. S., Z. Li, et al., Am J Pathol 2001, 159(6), 2167–77), juvenile onset diabetes, lupus, asthma (Cimerman, N., P. M. Brguljan, et al., Pflugers Arch 2001, 442(6 Suppl 1), R204–6), tissue rejection, Alzheimer's disease (Lemere, C. A., J. S. Munger, et al., Am J Pathol 1995, 146(4), 848–60), Parkinson's disease (Liu, Y., L. Fallon, et al., Cell 2002, 111(2), 209–18), neuronal degeneration, shock (Jaeschke, H., M. A. Fisher, et al., J Immunol 1998, 160(7), 3480–6), cancer (Fernandez, P. L., X. Farre, et al., Int J Cancer 2001, 95(1), 51–5), malaria (Malhotra, P., P. V. Dasaradhi, et al., Mol Microbiol 2002, 45(5), 1245–54), Chagas (Eakin, A. E., A. A. Mills, et al., J Biol Chem 1992, 267(11), 7411–20), leishmaniasis, shistosomiasis, and African trypanosomiasis (Caffrey, C. R., S. Scory, et al., Curr Drug Targets 2000, 1(2), 155–62; Lalmanach, G., A. Boulange, et al., Biol Chem 2002, 383(5), 739–49).
Cathepsins are a subclass of cysteine protease that belong to the enzyme classification EC 3.4.22 (Barrett, A. J., N. D. Rawlings, et al., Handbook of proteolytic enzymes. London, Academic Press). Cathepsins play a major role in lysosomal, endosomal, and extracellular protein degradation and have thus been implicated in many disease processes. For example, Cathepsin B [EC 3.4.22.1] has been postulated to play a role in tumor metastasis (Berquin, I. M. and B. F. Sloane Adv Exp Med Biol 1996, 389, 281–94).
Cathepsin S [EC 3.4.22.27] is largely expressed in professional antigen presenting cells such as macrophages and dendritic cells. Cathepsin S has been shown to be required for proper MHC class II antigen presentation (Shi, G. P., J. A. Villadangos, et al., Immunity 1999, 10(2) 197–206). As a result of its non-redundant role in MHC class II antigen presentation, cathepsin S has been associated with inflammation, arthritis, and atherosclerosis. The selective expression of cathepsin K [EC 3.4.22.38] in osteoclasts coupled with the ability of cathepsin K to degrade type I collagen suggests that it plays a role in normal and pathogenic bone remodeling (Bromme, D., K. Okamoto, et al., J Biol Chem 1996, 271(4), 2126–32). There is a need in the art for compounds and methods that selectively inhibit specific cysteine proteases for treating several pathogenic disorders in mammals. The present invention satisfies these and other needs.